From b27f973bd368619235ff19f706afb28b81c731e7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 4 Apr 2006 13:09:28 +0000
Subject: [PATCH] Draw threshold over graph

---
 src/jalview/gui/AnnotationPanel.java |   54 ++++++++++++++++------------------
 1 file changed, 25 insertions(+), 29 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index c5708ee..1b4a230 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -958,21 +958,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.setColor(Color.gray);
       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
 
-
-      if(aa.threshold!=null)
-      {
-          g.setColor(aa.threshold.colour);
-          Graphics2D g2 = (Graphics2D)g;
-          g2.setStroke(new BasicStroke(1,
-                                        BasicStroke.CAP_SQUARE,
-                                        BasicStroke.JOIN_ROUND, 3f,
-                                        new float[] { 5f, 3f }, 0f));
-
-          y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
-          g2.setStroke(new BasicStroke());
-      }
-
       eRes = Math.min(eRes, aa.annotations.length);
 
       int column = sRes;
@@ -1006,6 +991,19 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
           x += av.charWidth;
        }
+       if(aa.threshold!=null)
+       {
+           g.setColor(aa.threshold.colour);
+           Graphics2D g2 = (Graphics2D)g;
+           g2.setStroke(new BasicStroke(1,
+                                         BasicStroke.CAP_SQUARE,
+                                         BasicStroke.JOIN_ROUND, 3f,
+                                         new float[] { 5f, 3f }, 0f));
+
+           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
+           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+           g2.setStroke(new BasicStroke());
+      }
     }
 
     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
@@ -1022,20 +1020,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       float range = max - min;
 
-      if(aa.threshold!=null)
-      {
-          g.setColor(aa.threshold.colour);
-          Graphics2D g2 = (Graphics2D)g;
-          g2.setStroke(new BasicStroke(1,
-                                        BasicStroke.CAP_SQUARE,
-                                        BasicStroke.JOIN_ROUND, 3f,
-                                        new float[] { 5f, 3f }, 0f));
-
-          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
-          g2.setStroke(new BasicStroke());
-      }
-
       y1 = y2 = y;
 
       if(min<0)
@@ -1082,7 +1066,19 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
           x += av.charWidth;
       }
+      if(aa.threshold!=null)
+      {
+          g.setColor(aa.threshold.colour);
+          Graphics2D g2 = (Graphics2D)g;
+          g2.setStroke(new BasicStroke(1,
+                                        BasicStroke.CAP_SQUARE,
+                                        BasicStroke.JOIN_ROUND, 3f,
+                                        new float[] { 5f, 3f }, 0f));
 
+          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
+          g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+          g2.setStroke(new BasicStroke());
+      }
     }
 
     // used by overview window
-- 
1.7.10.2